Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr2
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 50190067
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 915496 characters in sequence are not A, C, G, or T
File 123 of 161
Found at i:38928738 original size:23 final size:23
Alignment explanation
Indices: 38928708--38928753 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
38928698 AGGATTTGCA
38928708 TATATTTCCCATACAATCAAGTT
1 TATATTTCCCATACAATCAAGTT
38928731 TATATTTCCCATACAATCAAGTT
1 TATATTTCCCATACAATCAAGTT
38928754 CCATCAACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.22, G:0.04, T:0.39
Consensus pattern (23 bp):
TATATTTCCCATACAATCAAGTT
Found at i:38929297 original size:20 final size:20
Alignment explanation
Indices: 38929252--38929291 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
38929242 TTAATAACTT
*
38929252 AATTAAAATAAGGTTTATTA
1 AATTAAAATAAGGTTAATTA
*
38929272 AATTAAAGTAAGGTTAATTA
1 AATTAAAATAAGGTTAATTA
38929292 TGTTAATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (20 bp):
AATTAAAATAAGGTTAATTA
Found at i:38930654 original size:243 final size:243
Alignment explanation
Indices: 38930225--38930700 Score: 702
Period size: 243 Copynumber: 2.0 Consensus size: 243
38930215 TAGTGTATAG
*
38930225 GATTGAAAATTTGATATGTGTATTATACTCTAAACAGAATTAAAATTTGATACCCTATTAACTAG
1 GATTGAAAAATTGATATGTGTATTATACTCTAAACAGAATTAAAATTTGATACCCTATTAACTAG
* * * *
38930290 TCGGGTTGAGTTGGATATAATTGGCATGTCATAGGATTGGATTGAGTATGGGATTATGCGCTTAT
66 TCGGATTGAGTTGGATATAATTGGCATGCCATAGGATTGGATTAAGTACGGGATTATGCGCTTAT
* * * *
38930355 ACCCCAGGATGCATTTCATGTGCTAGATATACACTTATGCACCAAGCTGTACCTTGTGTATCAGG
131 ACCCCAGGATGCATTTCATGTACTAGATATACACTTATGCACCAAGATGCACCTTGTGTACCAGG
* * * *
38930420 TATGCGTCTTGTACGTCAGGATGTACTTCGATGCCAGTTTGGTGTGTT
196 TATGCATCTTGTACGTCAAGATGCACTCCGATGCCAGTTTGGTGTGTT
* ** *
38930468 GATTGAAAAATTGATATGTGTATTATATTCTAAATGGAATTGAAATTTGATACCCTATTAACTAG
1 GATTGAAAAATTGATATGTGTATTATACTCTAAACAGAATTAAAATTTGATACCCTATTAACTAG
** * *
38930533 T-GGAATTGAGTTGGATATGGTTGGCATGCCATAGGATTGGATTAAGTACGGGATTATGTGTTTA
66 TCGG-ATTGAGTTGGATATAATTGGCATGCCATAGGATTGGATTAAGTACGGGATTATGCGCTTA
* * * * *
38930597 TACGCCAGGATGCATTTCATGTACTAGATATACGCTTGTGCGCCAAGATGCACCTTGTGTGCCAG
130 TACCCCAGGATGCATTTCATGTACTAGATATACACTTATGCACCAAGATGCACCTTGTGTACCAG
38930662 GTATGCATCTTGTACGTCAAGATGCACTCCGATGCCAGT
195 GTATGCATCTTGTACGTCAAGATGCACTCCGATGCCAGT
38930701 CAAGTTAATA
Statistics
Matches: 206, Mismatches: 26, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
242 2 0.01
243 204 0.99
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.34
Consensus pattern (243 bp):
GATTGAAAAATTGATATGTGTATTATACTCTAAACAGAATTAAAATTTGATACCCTATTAACTAG
TCGGATTGAGTTGGATATAATTGGCATGCCATAGGATTGGATTAAGTACGGGATTATGCGCTTAT
ACCCCAGGATGCATTTCATGTACTAGATATACACTTATGCACCAAGATGCACCTTGTGTACCAGG
TATGCATCTTGTACGTCAAGATGCACTCCGATGCCAGTTTGGTGTGTT
Found at i:38930673 original size:20 final size:19
Alignment explanation
Indices: 38930631--38930688 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 19
38930621 TAGATATACG
38930631 CTTGTGCGCCAAGATGCAC
1 CTTGTGCGCCAAGATGCAC
* * *
38930650 CTTGTGTGCCAGGTATGCAT
1 CTTGTGCGCCAAG-ATGCAC
* *
38930670 CTTGTACGTCAAGATGCAC
1 CTTGTGCGCCAAGATGCAC
38930689 TCCGATGCCA
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.28
Consensus pattern (19 bp):
CTTGTGCGCCAAGATGCAC
Found at i:38935157 original size:22 final size:20
Alignment explanation
Indices: 38935117--38935158 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
38935107 AAAAAAAACC
*
38935117 AAAATAAAAGAAAAGAGAAA
1 AAAATAAAAGAAAACAGAAA
38935137 AAAATAGAAAGAAAAACAGAAA
1 AAAATA-AAAG-AAAACAGAAA
38935159 TCTAATTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 6 0.32
21 4 0.21
22 9 0.47
ACGTcount: A:0.79, C:0.02, G:0.14, T:0.05
Consensus pattern (20 bp):
AAAATAAAAGAAAACAGAAA
Found at i:38936394 original size:45 final size:45
Alignment explanation
Indices: 38936323--38936472 Score: 124
Period size: 45 Copynumber: 3.3 Consensus size: 45
38936313 GCCAGTACAT
*
38936323 GAAGACAAGATCTACTTTTTCCTTTGATCTGCTTCGCCACCAGTATGG
1 GAAGGCAAGATCTAC---TTCCTTTGATCTGCTTCGCCACCAGTATGG
** * *** ** ***
38936371 GAAGGCAAGAT-TTGTTACCTTTGATCTACTTC-ATGCTGGTACAT
1 GAAGGCAAGATCTACTT-CCTTTGATCTGCTTCGCCACCAGTATGG
* *
38936415 GAAGACAAGATCTACTTTCTTTGATCTGCTTCGCCACCAGTATGG
1 GAAGGCAAGATCTACTTCCTTTGATCTGCTTCGCCACCAGTATGG
38936460 GAAGGCAAGATCT
1 GAAGGCAAGATCT
38936473 GCTGTTTTTT
Statistics
Matches: 73, Mismatches: 26, Indels: 9
0.68 0.24 0.08
Matches are distributed among these distances:
44 29 0.40
45 33 0.45
47 1 0.01
48 10 0.14
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.32
Consensus pattern (45 bp):
GAAGGCAAGATCTACTTCCTTTGATCTGCTTCGCCACCAGTATGG
Found at i:38936394 original size:92 final size:89
Alignment explanation
Indices: 38936297--38936470 Score: 294
Period size: 89 Copynumber: 1.9 Consensus size: 89
38936287 GACCTGATGT
38936297 CTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTACTTTTTCCTTTGATCTGCTTCGCCA
1 CTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTAC--TTT-CTTTGATCTGCTTCGCCA
38936362 CCAGTATGGGAAGGCAAGATTTGTTAC
63 CCAGTATGGGAAGGCAAGATTTGTTAC
* **
38936389 CTTTGATCTACTTCATGCTGGTACATGAAGACAAGATCTACTTTCTTTGATCTGCTTCGCCACCA
1 CTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTACTTTCTTTGATCTGCTTCGCCACCA
38936454 GTATGGGAAGGCAAGAT
66 GTATGGGAAGGCAAGAT
38936471 CTGCTGTTTT
Statistics
Matches: 79, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
89 38 0.48
90 3 0.04
92 38 0.48
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (89 bp):
CTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTACTTTCTTTGATCTGCTTCGCCACCA
GTATGGGAAGGCAAGATTTGTTAC
Found at i:38971413 original size:51 final size:51
Alignment explanation
Indices: 38971357--38971454 Score: 153
Period size: 51 Copynumber: 1.9 Consensus size: 51
38971347 AATTATTTTC
38971357 TCAATTTGCTCTCAATTTCCT-TCCAAATTTCTCTCAAATCCATATTTAATT
1 TCAATTTGCTCTCAATTTCCTCT-CAAATTTCTCTCAAATCCATATTTAATT
* * *
38971408 TCAATTTGCTCTCAATTTCCTCTTAAATTTCTCTTAAATCCCTATTT
1 TCAATTTGCTCTCAATTTCCTCTCAAATTTCTCTCAAATCCATATTT
38971455 TTAATTATTT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
51 42 0.98
52 1 0.02
ACGTcount: A:0.26, C:0.26, G:0.02, T:0.47
Consensus pattern (51 bp):
TCAATTTGCTCTCAATTTCCTCTCAAATTTCTCTCAAATCCATATTTAATT
Found at i:38973812 original size:21 final size:21
Alignment explanation
Indices: 38973783--38974027 Score: 337
Period size: 21 Copynumber: 11.5 Consensus size: 21
38973773 CCCTAACCCT
*
38973783 AAACTCTAACCCTTAACTTAA
1 AAACCCTAACCCTTAACTTAA
* *
38973804 AAACCCTAAACCCTTAAGTTAT
1 AAACCCT-AACCCTTAACTTAA
* * *
38973826 AAACCCAAACTCTTAAGTTAA
1 AAACCCTAACCCTTAACTTAA
*
38973847 AAACCCTAAATCCTTAACTTAA
1 AAACCCT-AACCCTTAACTTAA
38973869 AAACCCTAACCCTTAACTTAA
1 AAACCCTAACCCTTAACTTAA
38973890 AAACCCTAAGCCCTTAACTTAA
1 AAACCCTAA-CCCTTAACTTAA
* * *
38973912 ATACCCTAACTCTTAACCTAA
1 AAACCCTAACCCTTAACTTAA
*
38973933 AAACCTTAACCCTTAACTTAA
1 AAACCCTAACCCTTAACTTAA
*
38973954 AAACCTTAAACCCTTAACTTAA
1 AAACCCT-AACCCTTAACTTAA
*
38973976 ATACCCTAACCCTTAACTTAA
1 AAACCCTAACCCTTAACTTAA
38973997 AAACCCTAACCCTTAACTTAA
1 AAACCCTAACCCTTAACTTAA
38974018 AAACCCTAAC
1 AAACCCTAAC
38974028 TGTATTACTT
Statistics
Matches: 199, Mismatches: 21, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
21 124 0.62
22 75 0.38
ACGTcount: A:0.43, C:0.30, G:0.01, T:0.26
Consensus pattern (21 bp):
AAACCCTAACCCTTAACTTAA
Found at i:38973841 original size:43 final size:43
Alignment explanation
Indices: 38973783--38974026 Score: 339
Period size: 43 Copynumber: 5.7 Consensus size: 43
38973773 CCCTAACCCT
* * *
38973783 AAACTCTAACCCTTAACTTAAAAACCCTAAACCCTTAAGTTAT
1 AAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
* * * *
38973826 AAACCCAAACTCTTAAGTTAAAAACCCTAAATCCTTAACTTAA
1 AAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
*
38973869 AAACCCTAACCCTTAACTTAAAAACCCTAAGCCCTTAACTTAA
1 AAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
* * * *
38973912 ATACCCTAACTCTTAACCTAAAAA-CCTTAACCCTTAACTTAA
1 AAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
* *
38973954 AAACCTTAAACCCTTAACTTAAATACCCT-AACCCTTAACTTAA
1 AAACCCT-AACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
38973997 AAACCCTAACCCTTAACTTAAAAACCCTAA
1 AAACCCTAACCCTTAACTTAAAAACCCTAA
38974027 CTGTATTACT
Statistics
Matches: 174, Mismatches: 24, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
42 41 0.24
43 130 0.75
44 3 0.02
ACGTcount: A:0.43, C:0.30, G:0.01, T:0.26
Consensus pattern (43 bp):
AAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
Found at i:38973928 original size:64 final size:64
Alignment explanation
Indices: 38973788--38974026 Score: 354
Period size: 64 Copynumber: 3.7 Consensus size: 64
38973778 ACCCTAAACT
* * * * *
38973788 CTAACCCTTAACTTAAAAACCCTAAACCCTTAAGTTATAAACCC-AAACTCTTAAGTTAAAAACC
1 CTAACCCTTAACTTAAAAACCCT-AACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAATACC
* *
38973852 CTAAATCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACCCTAAGCCCTTAACTTAAATACC
1 CT-AACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAATACC
* * * *
38973917 CTAACTCTTAACCTAAAAACCTTAACCCTTAACTTAAAAACCTTAAACCCTTAACTTAAATACC
1 CTAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAATACC
38973981 CTAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACCCTAA
1 CTAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACCCTAA
38974027 CTGTATTACT
Statistics
Matches: 156, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
64 118 0.76
65 38 0.24
ACGTcount: A:0.43, C:0.30, G:0.01, T:0.26
Consensus pattern (64 bp):
CTAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAATACC
Found at i:38974039 original size:27 final size:27
Alignment explanation
Indices: 38974008--38974074 Score: 125
Period size: 27 Copynumber: 2.5 Consensus size: 27
38973998 AACCCTAACC
38974008 CTTAACTTAAAAACCCTAACTGTATTA
1 CTTAACTTAAAAACCCTAACTGTATTA
*
38974035 CTTAACTTAAAAACCCTAACTGTATTC
1 CTTAACTTAAAAACCCTAACTGTATTA
38974062 CTTAACTTAAAAA
1 CTTAACTTAAAAA
38974075 GCCTTAATTA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.42, C:0.22, G:0.03, T:0.33
Consensus pattern (27 bp):
CTTAACTTAAAAACCCTAACTGTATTA
Found at i:38974317 original size:22 final size:21
Alignment explanation
Indices: 38974277--38974322 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
38974267 TTTTTTCTAA
* *
38974277 AACCCTAAAAACCTTAAACCCT
1 AACCCTAAAAACC-CAAAACCT
38974299 AACCCTAAAAACCCAAAACCT
1 AACCCTAAAAACCCAAAACCT
38974320 AAC
1 AAC
38974323 GTTGGAGGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.50, C:0.37, G:0.00, T:0.13
Consensus pattern (21 bp):
AACCCTAAAAACCCAAAACCT
Found at i:38977007 original size:43 final size:43
Alignment explanation
Indices: 38976959--38977040 Score: 114
Period size: 43 Copynumber: 1.9 Consensus size: 43
38976949 GATTCTGTTA
* *
38976959 TGTG-TTATCGTGTAAGACCAC-ATTTGGGACATTGGCATCAACC
1 TGTGTTTA-CGTGTAAGACC-CTATCTGGGACAGTGGCATCAACC
38977002 TGTGTTTACGTGTAAGACCCTATCTGGGACAGTGGCATC
1 TGTGTTTACGTGTAAGACCCTATCTGGGACAGTGGCATC
38977041 GTTATATGAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
42 1 0.03
43 31 0.89
44 3 0.09
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (43 bp):
TGTGTTTACGTGTAAGACCCTATCTGGGACAGTGGCATCAACC
Found at i:38985524 original size:17 final size:18
Alignment explanation
Indices: 38985488--38985531 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
38985478 AAACAAAATT
38985488 TATTTTATAATAAGATAA
1 TATTTTATAATAAGATAA
38985506 TATTTTATAATAA-ATAA
1 TATTTTATAATAAGATAA
*
38985523 TATATTATA
1 TATTTTATA
38985532 TAGATTTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
17 12 0.48
18 13 0.52
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (18 bp):
TATTTTATAATAAGATAA
Found at i:38986294 original size:23 final size:23
Alignment explanation
Indices: 38986242--38986295 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
38986232 AAGATTTAAA
* *
38986242 AAAATACTCATATTTATATTATT
1 AAAATATTCATATTTATACTATT
*
38986265 AATATATTCATATTTTATACTA-T
1 AAAATATTCATA-TTTATACTATT
38986288 AAAATATT
1 AAAATATT
38986296 TTACTAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 18 0.69
24 8 0.31
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.48
Consensus pattern (23 bp):
AAAATATTCATATTTATACTATT
Found at i:38986413 original size:19 final size:20
Alignment explanation
Indices: 38986389--38986441 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 20
38986379 AATTTAAAAC
* *
38986389 TATTATTAAAGTTAAAATT-
1 TATTATTAAAATAAAAATTG
38986408 TATTATTAAAATAAAAATTG
1 TATTATTAAAATAAAAATTG
*
38986428 TAATATT-AAATAAA
1 TATTATTAAAATAAA
38986442 CTTGTTAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 24 0.80
20 6 0.20
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.42
Consensus pattern (20 bp):
TATTATTAAAATAAAAATTG
Found at i:38993887 original size:19 final size:20
Alignment explanation
Indices: 38993834--38993887 Score: 51
Period size: 19 Copynumber: 2.8 Consensus size: 20
38993824 AAAAAACATA
*
38993834 ATAATAAATATAAT-ATTAAT
1 ATAA-AAATAAAATAATTAAT
*
38993854 ATTAAAAAT-ATATAATT-AT
1 A-TAAAAATAAAATAATTAAT
38993873 ATAAAAATAAAATAA
1 ATAAAAATAAAATAA
38993888 AATCCTTCAC
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
18 7 0.25
19 10 0.36
20 8 0.29
21 3 0.11
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
ATAAAAATAAAATAATTAAT
Found at i:38994870 original size:22 final size:23
Alignment explanation
Indices: 38994844--38995100 Score: 117
Period size: 22 Copynumber: 11.0 Consensus size: 23
38994834 ATTTTCACAC
*
38994844 CAAAATTTGGACAGCATATATA-
1 CAAAATTTGGACAGCATATACAT
*
38994866 CAAAATTTGGACTGCATTTATACAT
1 CAAAATTTGGACAGCA--TATACAT
38994891 CAAAATTT-GACAGCATATACAT
1 CAAAATTTGGACAGCATATACAT
* ** * *
38994913 -AAATAATTGGATTGTATTTGTACAT
1 CAAA-ATTTGGACAGCA--TATACAT
38994938 CAAAATTT-GACAGCATATACAT
1 CAAAATTTGGACAGCATATACAT
**
38994960 -ATATAA-TTGGACTCCATTTATACAT
1 CA-A-AATTTGGACAGCA--TATACAT
*
38994985 CAAAATTT-GACAGCATACACAT
1 CAAAATTTGGACAGCATATACAT
* *
38995007 -ATATAA-TTGGACTGCATCTGTACAT
1 CA-A-AATTTGGACAGCA--TATACAT
*
38995032 CAAAATTT-GACAGCATACACAT
1 CAAAATTTGGACAGCATATACAT
* **
38995054 -ATATAA-TTGAACTCCATTTATACAT
1 CA-A-AATTTGGACAGCA--TATACAT
*
38995079 CAAAATTT-GATAGCATATACAT
1 CAAAATTTGGACAGCATATACAT
38995101 TCATTTACTC
Statistics
Matches: 174, Mismatches: 32, Indels: 58
0.66 0.12 0.22
Matches are distributed among these distances:
21 6 0.03
22 58 0.33
23 25 0.14
24 35 0.20
25 44 0.25
26 6 0.03
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.33
Consensus pattern (23 bp):
CAAAATTTGGACAGCATATACAT
Found at i:38994897 original size:47 final size:45
Alignment explanation
Indices: 38994844--38995097 Score: 292
Period size: 47 Copynumber: 5.4 Consensus size: 45
38994834 ATTTTCACAC
* *
38994844 CAAAATTTGGACAGCATATATACAAAATTTGGACTGCATTTATACAT
1 CAAAATTT-GACAGCATATATATATAA-TTGGACTGCATTTATACAT
* * * *
38994891 CAAAATTTGACAGCATATACATAAATAATTGGATTGTATTTGTACAT
1 CAAAATTTGACAGCATAT--ATATATAATTGGACTGCATTTATACAT
*
38994938 CAAAATTTGACAGCATATACATATATAATTGGACTCCATTTATACAT
1 CAAAATTTGACAGCATAT--ATATATAATTGGACTGCATTTATACAT
* * *
38994985 CAAAATTTGACAGCATACACATATATAATTGGACTGCATCTGTACAT
1 CAAAATTTGACAGCAT--ATATATATAATTGGACTGCATTTATACAT
* * *
38995032 CAAAATTTGACAGCATACACATATATAATTGAACTCCATTTATACAT
1 CAAAATTTGACAGCAT--ATATATATAATTGGACTGCATTTATACAT
*
38995079 CAAAATTTGATAGCATATA
1 CAAAATTTGACAGCATATA
38995098 CATTCATTTA
Statistics
Matches: 183, Mismatches: 20, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
45 2 0.01
46 10 0.05
47 164 0.90
48 6 0.03
49 1 0.01
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.33
Consensus pattern (45 bp):
CAAAATTTGACAGCATATATATATAATTGGACTGCATTTATACAT
Found at i:38994971 original size:94 final size:94
Alignment explanation
Indices: 38994844--38995100 Score: 383
Period size: 94 Copynumber: 2.7 Consensus size: 94
38994834 ATTTTCACAC
* * *
38994844 CAAAATTTGGACAGCATAT--ATACAAAATTTGGACTGCATTTATACATCAAAATTTGACAGCAT
1 CAAAATTT-GACAGCATATACATATATAA-TTGGACTCCATTTATACATCAAAATTTGACAGCAT
* * *
38994907 ATACATAAATAATTGGATTGTATTTGTACAT
64 ATACATAAATAATTGGACTGCATCTGTACAT
*
38994938 CAAAATTTGACAGCATATACATATATAATTGGACTCCATTTATACATCAAAATTTGACAGCATAC
1 CAAAATTTGACAGCATATACATATATAATTGGACTCCATTTATACATCAAAATTTGACAGCATAT
*
38995003 ACATATATAATTGGACTGCATCTGTACAT
66 ACATAAATAATTGGACTGCATCTGTACAT
* * *
38995032 CAAAATTTGACAGCATACACATATATAATTGAACTCCATTTATACATCAAAATTTGATAGCATAT
1 CAAAATTTGACAGCATATACATATATAATTGGACTCCATTTATACATCAAAATTTGACAGCATAT
38995097 ACAT
66 ACAT
38995101 TCATTTACTC
Statistics
Matches: 149, Mismatches: 12, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
93 10 0.07
94 133 0.89
95 6 0.04
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.33
Consensus pattern (94 bp):
CAAAATTTGACAGCATATACATATATAATTGGACTCCATTTATACATCAAAATTTGACAGCATAT
ACATAAATAATTGGACTGCATCTGTACAT
Found at i:38994978 original size:141 final size:140
Alignment explanation
Indices: 38994840--38995100 Score: 362
Period size: 141 Copynumber: 1.9 Consensus size: 140
38994830 TAGCATTTTC
* *
38994840 ACACCAAAATTTGGACAGCAT-ATATACAAAATTTGGACTGCATTTATACATCAAAATTTGACAG
1 ACACCAAAATTT-GACAGCATAACATACAAAA-TTGGACTGCATCTATACATCAAAATTTGACAG
* * * ** *
38994904 CATATACATAAATAATTGGATTGTATTTGTACATCAAAATTTGACAGCATATACATATATAATTG
64 CATACACATAAATAATTGAACTCCATTTATACATCAAAATTTGACAGCATATACATATATAATTG
38994969 GACTCCATTTAT
129 GACTCCATTTAT
* * * *
38994981 ACATCAAAATTTGACAGCATACACATATATAATTGGACTGCATCTGTACATCAAAATTTGACAGC
1 ACACCAAAATTTGACAGCATA-ACATACAAAATTGGACTGCATCTATACATCAAAATTTGACAGC
* *
38995046 ATACACATATATAATTGAACTCCATTTATACATCAAAATTTGATAGCATATACAT
65 ATACACATAAATAATTGAACTCCATTTATACATCAAAATTTGACAGCATATACAT
38995101 TCATTTACTC
Statistics
Matches: 104, Mismatches: 14, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
140 8 0.08
141 89 0.86
142 7 0.07
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.32
Consensus pattern (140 bp):
ACACCAAAATTTGACAGCATAACATACAAAATTGGACTGCATCTATACATCAAAATTTGACAGCA
TACACATAAATAATTGAACTCCATTTATACATCAAAATTTGACAGCATATACATATATAATTGGA
CTCCATTTAT
Found at i:38995023 original size:23 final size:23
Alignment explanation
Indices: 38994941--38995062 Score: 74
Period size: 23 Copynumber: 5.2 Consensus size: 23
38994931 TGTACATCAA
* *
38994941 AATTTGACAGCATATACATATAT
1 AATTGGACAGCATACACATATAT
** *
38994964 AATTGGACTCCATTTATACATCA-A-
1 AATTGGACAGCA--TACACAT-ATAT
*
38994988 AATTTGACAGCATACACATATAT
1 AATTGGACAGCATACACATATAT
*
38995011 AATTGGACTGCAT-CTGTACATCA-A-
1 AATTGGACAGCATAC---ACAT-ATAT
*
38995035 AATTTGACAGCATACACATATAT
1 AATTGGACAGCATACACATATAT
38995058 AATTG
1 AATTG
38995063 AACTCCATTT
Statistics
Matches: 75, Mismatches: 12, Indels: 24
0.68 0.11 0.22
Matches are distributed among these distances:
21 2 0.03
22 13 0.17
23 24 0.32
24 20 0.27
25 14 0.19
26 2 0.03
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.32
Consensus pattern (23 bp):
AATTGGACAGCATACACATATAT
Found at i:38995374 original size:14 final size:15
Alignment explanation
Indices: 38995336--38995384 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
38995326 TCACCATGCA
* *
38995336 CATATATATACATTAC
1 CATATAAATAC-TAAC
38995352 CATATAAATACTAAC
1 CATATAAATACTAAC
38995367 CATA-AAATACTAATC
1 CATATAAATACTAA-C
38995382 CAT
1 CAT
38995385 GATTAAAGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
14 9 0.30
15 11 0.37
16 10 0.33
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.31
Consensus pattern (15 bp):
CATATAAATACTAAC
Found at i:38996100 original size:43 final size:43
Alignment explanation
Indices: 38996035--38996156 Score: 160
Period size: 43 Copynumber: 2.8 Consensus size: 43
38996025 AGTACAATGC
* *
38996035 CAACGTCCCAGACGTGGTCTTACATGTAATCACATA-CCGATG
1 CAACGTCCCAGACGTGGTCTTACATGAAAACACATAGCCGATG
*
38996077 CAACTGTCCCAGACAG-GGTCTTACATGAAAACACA-AGTCGATG
1 CAAC-GTCCCAGAC-GTGGTCTTACATGAAAACACATAGCCGATG
*
38996120 CTGACGTCCCAGACGTGGTCTTACATGAAAACACATA
1 C-AACGTCCCAGACGTGGTCTTACATGAAAACACATA
38996157 TCGGAGTCCT
Statistics
Matches: 70, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
42 6 0.09
43 60 0.86
44 4 0.06
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.21
Consensus pattern (43 bp):
CAACGTCCCAGACGTGGTCTTACATGAAAACACATAGCCGATG
Found at i:38996815 original size:12 final size:12
Alignment explanation
Indices: 38996798--38996828 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
38996788 TATTAACCTT
38996798 TATATAAATATA
1 TATATAAATATA
*
38996810 TATATACATATA
1 TATATAAATATA
38996822 TATATAA
1 TATATAA
38996829 GGTTATACTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (12 bp):
TATATAAATATA
Found at i:38999643 original size:32 final size:32
Alignment explanation
Indices: 38999601--38999713 Score: 131
Period size: 32 Copynumber: 3.5 Consensus size: 32
38999591 TTAGAGTAAT
* * * *
38999601 TTTGTCATCATTTAACCACATTAAAGTTGATA
1 TTTGTTATCATTTCACAAAATTAAAGTTGATA
*
38999633 TTTGTTATCATTTCACAAAATTGAAGTTG-TAA
1 TTTGTTATCATTTCACAAAATTAAAGTTGAT-A
* *
38999665 TTTGTTA-CTATTTCATAAAATGAAAGTTGATA
1 TTTGTTATC-ATTTCACAAAATTAAAGTTGATA
38999697 TTTGTTATCATTTCACA
1 TTTGTTATCATTTCACA
38999714 GAACTGCGCG
Statistics
Matches: 68, Mismatches: 9, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
31 2 0.03
32 64 0.94
33 2 0.03
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.44
Consensus pattern (32 bp):
TTTGTTATCATTTCACAAAATTAAAGTTGATA
Found at i:39000220 original size:21 final size:21
Alignment explanation
Indices: 39000194--39000247 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
39000184 TGTATGGGGT
39000194 AAATAAAAAGAATATTTAGAA
1 AAATAAAAAGAATATTTAGAA
39000215 AAATAAAAAGAATATTTAGAA
1 AAATAAAAAGAATATTTAGAA
39000236 AAATAAAAAGAA
1 AAATAAAAAGAA
39000248 AACAGTAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.20
Consensus pattern (21 bp):
AAATAAAAAGAATATTTAGAA
Found at i:39000497 original size:7 final size:7
Alignment explanation
Indices: 39000487--39000512 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
39000477 GGAGTGGGGG
39000487 CTTTTGC
1 CTTTTGC
39000494 CTTTTGC
1 CTTTTGC
39000501 CTTTTGC
1 CTTTTGC
39000508 CTTTT
1 CTTTT
39000513 CATTAAAGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.27, G:0.12, T:0.62
Consensus pattern (7 bp):
CTTTTGC
Found at i:39006997 original size:7 final size:7
Alignment explanation
Indices: 39006987--39007042 Score: 112
Period size: 7 Copynumber: 8.0 Consensus size: 7
39006977 ATAATTTCTA
39006987 ATTTTTT
1 ATTTTTT
39006994 ATTTTTT
1 ATTTTTT
39007001 ATTTTTT
1 ATTTTTT
39007008 ATTTTTT
1 ATTTTTT
39007015 ATTTTTT
1 ATTTTTT
39007022 ATTTTTT
1 ATTTTTT
39007029 ATTTTTT
1 ATTTTTT
39007036 ATTTTTT
1 ATTTTTT
39007043 TGAAAGAAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 49 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (7 bp):
ATTTTTT
Found at i:39009390 original size:31 final size:30
Alignment explanation
Indices: 39009347--39009422 Score: 107
Period size: 31 Copynumber: 2.5 Consensus size: 30
39009337 GGGGCTCATT
* * *
39009347 ATTAATTCAATTTAATTACATTATGTAATA
1 ATTAATTTAATTTAATCACATTATATAATA
*
39009377 TTTTAATTTAATTTAATCACATTATATAATA
1 -ATTAATTTAATTTAATCACATTATATAATA
39009408 ATTAATTTAATTTAA
1 ATTAATTTAATTTAA
39009423 CTAATATATC
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
30 14 0.35
31 26 0.65
ACGTcount: A:0.43, C:0.05, G:0.01, T:0.50
Consensus pattern (30 bp):
ATTAATTTAATTTAATCACATTATATAATA
Found at i:39016413 original size:19 final size:19
Alignment explanation
Indices: 39016369--39016425 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
39016359 TCAATACCGA
*
39016369 TACAAAAATATCGACACTT
1 TACAAAAATATCGATACTT
*
39016388 TATAAAAAGTATCGATAC-T
1 TACAAAAA-TATCGATACTT
39016407 TACAAAAAATTATCGATAC
1 TAC-AAAAA-TATCGATAC
39016426 CTATTGGGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
19 10 0.31
20 22 0.69
ACGTcount: A:0.49, C:0.16, G:0.07, T:0.28
Consensus pattern (19 bp):
TACAAAAATATCGATACTT
Found at i:39018388 original size:18 final size:19
Alignment explanation
Indices: 39018345--39018391 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
39018335 TGTCTTTAAC
*
39018345 TAAAAATGAATGACCAATT
1 TAAAAATGAATGACCAATA
39018364 TAAAAATGAATG-CCAA-A
1 TAAAAATGAATGACCAATA
39018381 TAATAAATGAA
1 TAA-AAATGAA
39018392 AAATTTTTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 3 0.12
18 11 0.42
19 12 0.46
ACGTcount: A:0.57, C:0.09, G:0.11, T:0.23
Consensus pattern (19 bp):
TAAAAATGAATGACCAATA
Found at i:39022137 original size:15 final size:15
Alignment explanation
Indices: 39022082--39022138 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
39022072 ATTATATTAC
*
39022082 AAAATATTTTTTATT
1 AAAATATTTATTATT
* *
39022097 AATATATTTATAATTGT
1 AAAATATTTATTA-T-T
39022114 AATAAATATTTATTATT
1 -A-AAATATTTATTATT
39022131 AAAATATT
1 AAAATATT
39022139 AATATTCAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 17 0.52
16 2 0.06
17 2 0.06
18 2 0.06
19 10 0.30
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (15 bp):
AAAATATTTATTATT
Found at i:39023974 original size:37 final size:39
Alignment explanation
Indices: 39023899--39023974 Score: 95
Period size: 40 Copynumber: 2.0 Consensus size: 39
39023889 TCACACGAGT
* * *
39023899 AAAAAAAATTAGTTAAAATTAATGAAAGATAAAGGTAAA
1 AAAAAAAACTAGTTAAAAATAATGAAAGAGAAAGGTAAA
39023938 AAAAAAGAACTAGTTAAAAATAAT-AAA-AGAAA-GTAAA
1 AAAAAA-AACTAGTTAAAAATAATGAAAGAGAAAGGTAAA
39023975 GTTAAATAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 5 0.15
38 4 0.12
39 9 0.27
40 15 0.45
ACGTcount: A:0.67, C:0.01, G:0.12, T:0.20
Consensus pattern (39 bp):
AAAAAAAACTAGTTAAAAATAATGAAAGAGAAAGGTAAA
Found at i:39024636 original size:27 final size:27
Alignment explanation
Indices: 39024606--39024694 Score: 74
Period size: 28 Copynumber: 3.2 Consensus size: 27
39024596 TCATTTAATT
39024606 ATTTTTAATTTTAAAAAATATTTTTATA
1 ATTTTTAATTTT-AAAAATATTTTTATA
* * *
39024634 TTTTTTATAATTT-AAAAT-TTTTTAGTG
1 ATTTTTA-ATTTTAAAAATATTTTTA-TA
* * *
39024661 ATTTCTAATTTTTAAAAGTAGTTTTATA
1 ATTTTTAA-TTTTAAAAATATTTTTATA
39024689 ATTTTT
1 ATTTTT
39024695 TTAAATTTTT
Statistics
Matches: 46, Mismatches: 10, Indels: 10
0.70 0.15 0.15
Matches are distributed among these distances:
26 7 0.15
27 14 0.30
28 16 0.35
29 9 0.20
ACGTcount: A:0.35, C:0.01, G:0.04, T:0.60
Consensus pattern (27 bp):
ATTTTTAATTTTAAAAATATTTTTATA
Found at i:39024713 original size:56 final size:54
Alignment explanation
Indices: 39024606--39024712 Score: 126
Period size: 55 Copynumber: 1.9 Consensus size: 54
39024596 TCATTTAATT
* *
39024606 ATTTTTAATTTTAAAAAATATTTTTATATTTTTTATAATTTAAAATTTTTTAGTG
1 ATTTCTAATTTTAAAAAATAGTTTTATATTTTTTATAATTTAAAA-TTTTTAGTG
* *
39024661 ATTTCTAATTTTTAAAAGTAGTTTTATAATTTTTT-TAAATTTTTAAAATTTT
1 ATTTCTAATTTTAAAAAATAGTTTTAT-ATTTTTTAT-AA--TTTAAAATTTT
39024713 AAAGAATGAA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
55 24 0.55
56 9 0.20
57 4 0.09
58 7 0.16
ACGTcount: A:0.36, C:0.01, G:0.04, T:0.60
Consensus pattern (54 bp):
ATTTCTAATTTTAAAAAATAGTTTTATATTTTTTATAATTTAAAATTTTTAGTG
Found at i:39029978 original size:22 final size:22
Alignment explanation
Indices: 39029927--39029980 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
39029917 TTATTTTGAC
*
39029927 ATTTTAAAATTTTTTAACAATA
1 ATTTTAAAATTTTTTAACAAAA
* *
39029949 ATTGTAAATTTTTTTAA-AAAA
1 ATTTTAAAATTTTTTAACAAAA
39029970 ATCTTTAAAAT
1 AT-TTTAAAAT
39029981 AAATAAAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 5 0.19
22 21 0.81
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (22 bp):
ATTTTAAAATTTTTTAACAAAA
Found at i:39030101 original size:3 final size:3
Alignment explanation
Indices: 39030093--39030123 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
39030083 CTTTCACAAA
39030093 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
39030124 TCCATTCACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:39033521 original size:8 final size:9
Alignment explanation
Indices: 39033498--39033524 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
39033488 TAGTTGAACC
39033498 AATTTTTAT
1 AATTTTTAT
39033507 AATTTTTAT
1 AATTTTTAT
39033516 AATTTTTAT
1 AATTTTTAT
39033525 TTTGATTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
AATTTTTAT
Found at i:39043818 original size:52 final size:52
Alignment explanation
Indices: 39043740--39043846 Score: 178
Period size: 52 Copynumber: 2.1 Consensus size: 52
39043730 TCCACAGCTA
* *
39043740 AAGGCTGATTCCAATGGCGAAGTTTATGCTATAGAATCTATAGCCAAAAAGT
1 AAGGCCGATTCCAACGGCGAAGTTTATGCTATAGAATCTATAGCCAAAAAGT
* *
39043792 AAGGCCGATTCCAACGGCGAAGTTTATGTTGTAGAATCTATAGCCAAAAAGT
1 AAGGCCGATTCCAACGGCGAAGTTTATGCTATAGAATCTATAGCCAAAAAGT
39043844 AAG
1 AAG
39043847 TTTTACCTAC
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.25
Consensus pattern (52 bp):
AAGGCCGATTCCAACGGCGAAGTTTATGCTATAGAATCTATAGCCAAAAAGT
Found at i:39071744 original size:14 final size:15
Alignment explanation
Indices: 39071718--39071746 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
39071708 CAAGCCCCAT
39071718 TCTTTTCATTTTTCA
1 TCTTTTCATTTTTCA
39071733 TCTTTT-ATTTTTCA
1 TCTTTTCATTTTTCA
39071747 GCAACTAAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.14, C:0.17, G:0.00, T:0.69
Consensus pattern (15 bp):
TCTTTTCATTTTTCA
Found at i:39085197 original size:6 final size:6
Alignment explanation
Indices: 39085186--39085213 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
39085176 AACTGAATAA
39085186 ATTTAT ATTTAT ATTTAT ATTTAT ATTT
1 ATTTAT ATTTAT ATTTAT ATTTAT ATTT
39085214 GGATCAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
ATTTAT
Found at i:39095740 original size:29 final size:31
Alignment explanation
Indices: 39095675--39095744 Score: 81
Period size: 29 Copynumber: 2.3 Consensus size: 31
39095665 GTATAATTAT
** *
39095675 ATTAAATTATTTAAATATTATTTCATATTATA
1 ATTAAATT-TTTAAATAACATTTCATAGTATA
*
39095707 TTTAAATTTTTAAA-AACATTTCAT-GTATA
1 ATTAAATTTTTAAATAACATTTCATAGTATA
39095736 ATTAAATTT
1 ATTAAATTT
39095745 ATAATTAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
29 12 0.36
30 8 0.24
31 6 0.18
32 7 0.21
ACGTcount: A:0.43, C:0.04, G:0.01, T:0.51
Consensus pattern (31 bp):
ATTAAATTTTTAAATAACATTTCATAGTATA
Found at i:39096407 original size:31 final size:31
Alignment explanation
Indices: 39096369--39096434 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
39096359 CTCGTTAATG
* ** *
39096369 ATACTGACATGGCAAATGATGCTGATGTGGT
1 ATACTGACATGGCAAACGACACTGATGTGGC
39096400 ATACTGACATGGCAAACGACACTGATGTGGC
1 ATACTGACATGGCAAACGACACTGATGTGGC
39096431 ATAC
1 ATAC
39096435 CACATAGCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (31 bp):
ATACTGACATGGCAAACGACACTGATGTGGC
Found at i:39096465 original size:10 final size:10
Alignment explanation
Indices: 39096450--39096483 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
39096440 AGCAAAATTT
*
39096450 AAAAATTTTA
1 AAAAATTATA
39096460 AAAAATTATA
1 AAAAATTATA
39096470 AAAAA-TATA
1 AAAAATTATA
39096479 AAAAA
1 AAAAA
39096484 AAAATATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 9 0.39
10 14 0.61
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (10 bp):
AAAAATTATA
Found at i:39100604 original size:20 final size:19
Alignment explanation
Indices: 39100530--39100607 Score: 77
Period size: 20 Copynumber: 4.1 Consensus size: 19
39100520 AGAAATGAAA
* * *
39100530 AAAAATTGTAAAAATA-TA
1 AAAAATTATAAAATTATTT
39100548 AAAAATTATAATAATTATTT
1 AAAAATTATAA-AATTATTT
* * *
39100568 AGAAATTTTAAATTTATTT
1 AAAAATTATAAAATTATTT
39100587 AAAAATATATAAAATTATTT
1 AAAAAT-TATAAAATTATTT
39100607 A
1 A
39100608 TGCTCCAACT
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
18 10 0.21
19 16 0.33
20 22 0.46
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (19 bp):
AAAAATTATAAAATTATTT
Found at i:39101086 original size:20 final size:19
Alignment explanation
Indices: 39101063--39101133 Score: 58
Period size: 20 Copynumber: 3.6 Consensus size: 19
39101053 ATTAAAATCG
39101063 TAAAATATTATTTAAAAATA
1 TAAAA-ATTATTTAAAAATA
39101083 T-AAAATTA--TAAAAATTA
1 TAAAAATTATTTAAAAA-TA
* *
39101100 GTAAAACATTATTTAGAAATTT
1 -TAAAA-ATTATTTA-AAAATA
39101122 TAAAAATTATTT
1 TAAAAATTATTT
39101134 TATATATATA
Statistics
Matches: 42, Mismatches: 2, Indels: 14
0.72 0.03 0.24
Matches are distributed among these distances:
16 6 0.14
17 2 0.05
18 5 0.12
19 6 0.14
20 12 0.29
21 5 0.12
22 3 0.07
23 3 0.07
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.41
Consensus pattern (19 bp):
TAAAAATTATTTAAAAATA
Found at i:39101453 original size:19 final size:19
Alignment explanation
Indices: 39101408--39101454 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
39101398 ATTGCAATTT
39101408 TTTTAAAAA-CACAAAAAA
1 TTTTAAAAATCACAAAAAA
* * **
39101426 TTGTGAAAATCATTAAAAA
1 TTTTAAAAATCACAAAAAA
39101445 TTTTAAAAAT
1 TTTTAAAAAT
39101455 TGCAATCATT
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.32
Consensus pattern (19 bp):
TTTTAAAAATCACAAAAAA
Found at i:39101527 original size:14 final size:15
Alignment explanation
Indices: 39101508--39101536 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
39101498 GAAATTGTAA
39101508 AAATTAT-ATTTTTT
1 AAATTATAATTTTTT
39101522 AAATTATAATTTTTT
1 AAATTATAATTTTTT
39101537 TTTACAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
AAATTATAATTTTTT
Found at i:39101796 original size:18 final size:19
Alignment explanation
Indices: 39101767--39101808 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
39101757 AAATCTTATT
39101767 ATTTTTATAATTTTTAATC
1 ATTTTTATAATTTTTAATC
*
39101786 ATTTTTA-AATTTTTAATG
1 ATTTTTATAATTTTTAATC
39101804 ATTTT
1 ATTTT
39101809 CACAATATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (19 bp):
ATTTTTATAATTTTTAATC
Found at i:39101915 original size:40 final size:40
Alignment explanation
Indices: 39101863--39101941 Score: 92
Period size: 40 Copynumber: 2.0 Consensus size: 40
39101853 AATTACAGTT
*
39101863 TTTATAATTTTTAACA-AAATTTCAAAGAATTTT-TAAATAA
1 TTTATAATTTTTAAAACAAATTT-AAA-AATTTTCTAAATAA
*
39101903 TTTAT-ATATTTTAAAACAAATTTTAAAATTTTCTAAATA
1 TTTATAAT-TTTTAAAACAAATTTAAAAATTTTCTAAATA
39101942 TTTTTTACCA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
39 8 0.24
40 20 0.59
41 6 0.18
ACGTcount: A:0.47, C:0.05, G:0.01, T:0.47
Consensus pattern (40 bp):
TTTATAATTTTTAAAACAAATTTAAAAATTTTCTAAATAA
Found at i:39107981 original size:37 final size:37
Alignment explanation
Indices: 39107935--39108063 Score: 154
Period size: 37 Copynumber: 3.5 Consensus size: 37
39107925 TTCTACTCGT
* *
39107935 TTGAGCTTCACTCTGTATAACAATAGGATTTGATTGA
1 TTGAGCTTCATTCAGTATAACAATAGGATTTGATTGA
*
39107972 TTGAGCTTCATTCAATATAACAATAGGATTT-ACTTGA
1 TTGAGCTTCATTCAGTATAACAATAGGATTTGA-TTGA
* * * *
39108009 TTGAGCTTCATTCAGCATAAC-GTAGGATTTGCTCGA
1 TTGAGCTTCATTCAGTATAACAATAGGATTTGATTGA
* *
39108045 TTGAGCTTCTTTCCGTATA
1 TTGAGCTTCATTCAGTATA
39108064 TTAGTAGATA
Statistics
Matches: 79, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
36 28 0.35
37 51 0.65
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.38
Consensus pattern (37 bp):
TTGAGCTTCATTCAGTATAACAATAGGATTTGATTGA
Found at i:39111972 original size:21 final size:21
Alignment explanation
Indices: 39111946--39112053 Score: 153
Period size: 21 Copynumber: 5.1 Consensus size: 21
39111936 ATTGGGTGGA
*
39111946 TCAGCTCTCACGAGCTTCTGT
1 TCAGCTCTTACGAGCTTCTGT
*
39111967 TCAGCTCTTACGAGCTTCTAT
1 TCAGCTCTTACGAGCTTCTGT
* * *
39111988 TAAGCTCTTATGAGCTTTTGT
1 TCAGCTCTTACGAGCTTCTGT
* *
39112009 TCAGCTCTTATGAGTTTCTGT
1 TCAGCTCTTACGAGCTTCTGT
39112030 TCAGCTCTTACGAGCTTCTGT
1 TCAGCTCTTACGAGCTTCTGT
39112051 TCA
1 TCA
39112054 AATTTCGAGC
Statistics
Matches: 76, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 76 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.41
Consensus pattern (21 bp):
TCAGCTCTTACGAGCTTCTGT
Found at i:39111995 original size:42 final size:42
Alignment explanation
Indices: 39111948--39112070 Score: 151
Period size: 42 Copynumber: 3.0 Consensus size: 42
39111938 TGGGTGGATC
*
39111948 AGCTCTCACGAGCTTCTGTTCAGCTCTTACGAGCTTCTATTA
1 AGCTCTTACGAGCTTCTGTTCAGCTCTTACGAGCTTCTATTA
* * * * * *
39111990 AGCTCTTATGAGCTTTTGTTCAGCTCTTATGAGTTTCTGTTC
1 AGCTCTTACGAGCTTCTGTTCAGCTCTTACGAGCTTCTATTA
**
39112032 AGCTCTTACGAGCTTCTGTTCAAAT-TT-CGAGCTTCTATT
1 AGCTCTTACGAGCTTCTGTTCAGCTCTTACGAGCTTCTATT
39112071 GGTGTATTCG
Statistics
Matches: 67, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
40 9 0.13
41 2 0.03
42 56 0.84
ACGTcount: A:0.18, C:0.24, G:0.17, T:0.41
Consensus pattern (42 bp):
AGCTCTTACGAGCTTCTGTTCAGCTCTTACGAGCTTCTATTA
Found at i:39118224 original size:19 final size:19
Alignment explanation
Indices: 39118171--39118224 Score: 51
Period size: 19 Copynumber: 2.8 Consensus size: 19
39118161 ATCGCGTTCA
39118171 ATTTATTTCTAGTATTT-ATT
1 ATTTATTT-TA-TATTTAATT
*
39118191 -TTTATTTGA-ATTTTAATT
1 ATTTATTTTATA-TTTAATT
39118209 ATTTATTTTATATTTA
1 ATTTATTTTATATTTA
39118225 GATTTAATCT
Statistics
Matches: 28, Mismatches: 2, Indels: 9
0.72 0.05 0.23
Matches are distributed among these distances:
16 1 0.04
17 3 0.11
18 4 0.14
19 19 0.68
20 1 0.04
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.67
Consensus pattern (19 bp):
ATTTATTTTATATTTAATT
Found at i:39118575 original size:30 final size:31
Alignment explanation
Indices: 39118517--39118582 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 31
39118507 CATTTATTTA
*
39118517 AATGTATACAACTGAATCAAAATTAAAGTTT
1 AATGTATACAACTGAATCAAAATAAAAGTTT
* **
39118548 TATGTATACATTTGAA-CAAAATAAAAGTTT
1 AATGTATACAACTGAATCAAAATAAAAGTTT
39118578 AATGT
1 AATGT
39118583 GTATAATTAC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 17 0.57
31 13 0.43
ACGTcount: A:0.47, C:0.08, G:0.11, T:0.35
Consensus pattern (31 bp):
AATGTATACAACTGAATCAAAATAAAAGTTT
Found at i:39121156 original size:8 final size:8
Alignment explanation
Indices: 39121143--39121175 Score: 66
Period size: 8 Copynumber: 4.1 Consensus size: 8
39121133 ATTTTTGTGT
39121143 TCAATTTC
1 TCAATTTC
39121151 TCAATTTC
1 TCAATTTC
39121159 TCAATTTC
1 TCAATTTC
39121167 TCAATTTC
1 TCAATTTC
39121175 T
1 T
39121176 TCCGCTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (8 bp):
TCAATTTC
Found at i:39123179 original size:23 final size:23
Alignment explanation
Indices: 39123136--39123179 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
39123126 GAAATGTTAG
**
39123136 TTTAAAATTTGTTTAGTTTTAAT
1 TTTAAAATTTGTTTAAATTTAAT
39123159 TTTAAGAATTT-TTTAAATTTA
1 TTTAA-AATTTGTTTAAATTTA
39123180 TACATATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 13 0.72
24 5 0.28
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (23 bp):
TTTAAAATTTGTTTAAATTTAAT
Found at i:39136606 original size:22 final size:22
Alignment explanation
Indices: 39136580--39136623 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
39136570 AGATTGAAAC
39136580 CTTGAATTTATTCATTAAATCT
1 CTTGAATTTATTCATTAAATCT
39136602 CTTGAATTTATTCATTAAATCT
1 CTTGAATTTATTCATTAAATCT
39136624 GTTAGAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.14, G:0.05, T:0.50
Consensus pattern (22 bp):
CTTGAATTTATTCATTAAATCT
Found at i:39145934 original size:4 final size:4
Alignment explanation
Indices: 39145927--39145953 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
39145917 ATTATATATT
39145927 ATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATA
39145954 TGCAGTAGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:39150559 original size:8 final size:8
Alignment explanation
Indices: 39150546--39150583 Score: 76
Period size: 8 Copynumber: 4.8 Consensus size: 8
39150536 TAAATAGTTT
39150546 TAATAAAA
1 TAATAAAA
39150554 TAATAAAA
1 TAATAAAA
39150562 TAATAAAA
1 TAATAAAA
39150570 TAATAAAA
1 TAATAAAA
39150578 TAATAA
1 TAATAA
39150584 TTTATTATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 30 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (8 bp):
TAATAAAA
Found at i:39152645 original size:67 final size:68
Alignment explanation
Indices: 39152523--39152714 Score: 212
Period size: 67 Copynumber: 2.8 Consensus size: 68
39152513 AAGTAACAAT
* * ** *
39152523 TTCTTCACTATTTTTATTAAAAAGTTAATTTTAGTCACACACCGACTAGATAATACTCTCATAGC
1 TTCTTCACTATTTTCATT-AAAAGTTAATTTTAATCACACATTGACTAGAGAATACTCTCATAGC
39152588 TAAC
65 TAAC
* * *
39152592 -T-TTCACTATTTTCATTGAAAAGTTAATTTTAATCTCACATTGACTTGAGAATACTCTCATAGT
1 TTCTTCACTATTTTCATT-AAAAGTTAATTTTAATCACACATTGACTAGAGAATACTCTCATAGC
*
39152655 TCAC
65 TAAC
* * * *
39152659 TTCTTCACTA-TTTCATTAAAAATTATTTTTAATCCCACATT-AGCTAGAGAACACTC
1 TTCTTCACTATTTTCATTAAAAGTTAATTTTAATCACACATTGA-CTAGAGAATACTC
39152715 ACATGCTCAC
Statistics
Matches: 105, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
66 1 0.01
67 88 0.84
68 9 0.09
69 7 0.07
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (68 bp):
TTCTTCACTATTTTCATTAAAAGTTAATTTTAATCACACATTGACTAGAGAATACTCTCATAGCT
AAC
Found at i:39156054 original size:84 final size:84
Alignment explanation
Indices: 39155913--39156068 Score: 219
Period size: 84 Copynumber: 1.9 Consensus size: 84
39155903 GGCTCGTACA
* * *
39155913 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATATCGATGCCACAGTCCCAGATAG-GG
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAAACACATATCGATGCCACAGTCCCAGA-AGTGG
39155977 TCTTACACAAATCAAATACG
65 TCTTACACAAATCAAATACG
* *
39155997 ATGCCAATGTCCCAGACATGGTCTTACACGTAAACACA-AGTCGATGCCA-ACGTCCCAGACGTG
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAAACACATA-TCGATGCCACA-GTCCCAGAAGTG
39156060 GTCTTACAC
64 GTCTTACAC
39156069 GAAAANATCC
Statistics
Matches: 64, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
83 3 0.05
84 61 0.95
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.22
Consensus pattern (84 bp):
ATGCCAACGTCCCAGACATGGTCTTACACGTAAACACATATCGATGCCACAGTCCCAGAAGTGGT
CTTACACAAATCAAATACG
Found at i:39156068 original size:43 final size:42
Alignment explanation
Indices: 39155913--39156069 Score: 180
Period size: 43 Copynumber: 3.7 Consensus size: 42
39155903 GGCTCGTACA
* *
39155913 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAAACACA-ATCG
*
39155956 ATGCC-ACAGTCCCAGATAG-GGTCTTACAC--AAATCA-AATACG
1 ATGCCAAC-GTCCCAGA-CGTGGTCTTACACGTAAA-CACAAT-CG
* *
39155997 ATGCCAATGTCCCAGACATGGTCTTACACGTAAACACAAGTCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAAACACAA-TCG
39156040 ATGCCAACGTCCCAGACGTGGTCTTACACG
1 ATGCCAACGTCCCAGACGTGGTCTTACACG
39156070 AAAANATCCA
Statistics
Matches: 96, Mismatches: 8, Indels: 20
0.77 0.06 0.16
Matches are distributed among these distances:
40 2 0.02
41 28 0.29
42 7 0.07
43 57 0.59
44 2 0.02
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.22
Consensus pattern (42 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGTAAACACAATCG
Found at i:39159141 original size:20 final size:21
Alignment explanation
Indices: 39159101--39159142 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
39159091 ATTTAATTGA
* *
39159101 ATAAATCTTAATTAGTTAATT
1 ATAAATCTTAATTAATCAATT
39159122 ATAAA-CTTAATTAATCAATT
1 ATAAATCTTAATTAATCAATT
39159142 A
1 A
39159143 AGTGGGTGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (21 bp):
ATAAATCTTAATTAATCAATT
Found at i:39163059 original size:19 final size:20
Alignment explanation
Indices: 39163014--39163076 Score: 85
Period size: 19 Copynumber: 3.1 Consensus size: 20
39163004 ACTATTTTTA
39163014 TTAAAAA-TTAATTTTAATCC
1 TTAAAAAGTTAATTTTAAT-C
39163034 TTTAAAAAGTTAATTTTAA-C
1 -TTAAAAAGTTAATTTTAATC
*
39163054 TTAAAAGGTTAATTTTAATC
1 TTAAAAAGTTAATTTTAATC
39163074 TTA
1 TTA
39163077 CATTGGCTAG
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
19 17 0.44
20 5 0.13
21 7 0.18
22 10 0.26
ACGTcount: A:0.43, C:0.06, G:0.05, T:0.46
Consensus pattern (20 bp):
TTAAAAAGTTAATTTTAATC
Found at i:39163365 original size:71 final size:72
Alignment explanation
Indices: 39163219--39163395 Score: 195
Period size: 71 Copynumber: 2.5 Consensus size: 72
39163209 AAGTGACAAT
* * *
39163219 TTCTTCACTA-TTTCATTAAAAATTTTAATTTTAATCTTACATTGACCAAAGAAAATACTCTCCT
1 TTCTTCACTATTTTAATTAAAAAATTTAATTTTAATCCTACATTGACCAAAGAAAATACTCTCCT
**
39163283 AGTTCAC
66 AACTCAC
* * * *
39163290 TTCTTCACTATTTTAATTGAAAAAATTTAATTTAAATCCTACATTGA-C-TAGAGAGTACT-TCC
1 TTCTTCACTATTTTAATT-AAAAAATTTAATTTTAATCCTACATTGACCAAAGAAAATACTCTCC
39163352 ATAACTCAC
65 -TAACTCAC
* *
39163361 TTCTTTACTATTTTTATT-AAAAA-TTAATTTTAATC
1 TTCTTCACTATTTTAATTAAAAAATTTAATTTTAATC
39163396 TCTTAAAAAG
Statistics
Matches: 91, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
68 11 0.12
69 5 0.05
70 3 0.03
71 40 0.44
72 7 0.08
73 25 0.27
ACGTcount: A:0.36, C:0.17, G:0.05, T:0.43
Consensus pattern (72 bp):
TTCTTCACTATTTTAATTAAAAAATTTAATTTTAATCCTACATTGACCAAAGAAAATACTCTCCT
AACTCAC
Found at i:39163403 original size:21 final size:22
Alignment explanation
Indices: 39163377--39163417 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
39163367 ACTATTTTTA
39163377 TTAAAAA-TTAATTTTAATCTC
1 TTAAAAAGTTAATTTTAATCTC
39163398 TTAAAAAGTTAATTTTAATC
1 TTAAAAAGTTAATTTTAATC
39163418 CCAGATTTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.46
Consensus pattern (22 bp):
TTAAAAAGTTAATTTTAATCTC
Found at i:39165200 original size:25 final size:24
Alignment explanation
Indices: 39165158--39165204 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
39165148 GAGAATTATT
*
39165158 TAAAATTATTAAGAATTATAAAAAA
1 TAAAATGATTAAGAATTA-AAAAAA
39165183 TAAAATGATTAATG-ATTAAAAA
1 TAAAATGATTAA-GAATTAAAAA
39165205 TGATTAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 4 0.20
25 15 0.75
26 1 0.05
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (24 bp):
TAAAATGATTAAGAATTAAAAAAA
Found at i:39165343 original size:31 final size:31
Alignment explanation
Indices: 39165297--39165359 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
39165287 GAGTGGTTTC
*
39165297 TTAAATAATTATAAAAATGATAGGAAATTAT
1 TTAAATAATTATAAAAATGATAAGAAATTAT
* *
39165328 TTAAA-AATTATTAAAAATTATAAGCAATTAT
1 TTAAATAATTA-TAAAAATGATAAGAAATTAT
39165359 T
1 T
39165360 ATTTTTAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 5 0.18
31 23 0.82
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (31 bp):
TTAAATAATTATAAAAATGATAAGAAATTAT
Found at i:39166821 original size:13 final size:13
Alignment explanation
Indices: 39166803--39166833 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
39166793 AATTTAACTT
39166803 TTGTTTGGTTGGG
1 TTGTTTGGTTGGG
39166816 TTGTTTGGTTGGG
1 TTGTTTGGTTGGG
39166829 TTGTT
1 TTGTT
39166834 AGTAGTGAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.00, C:0.00, G:0.42, T:0.58
Consensus pattern (13 bp):
TTGTTTGGTTGGG
Found at i:39170350 original size:11 final size:11
Alignment explanation
Indices: 39170330--39170359 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
39170320 TTAAAATAAA
39170330 AAAAAGTATTTT
1 AAAAA-TATTTT
39170342 AAAAATATTTT
1 AAAAATATTTT
39170353 AAAAATA
1 AAAAATA
39170360 AAAAAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:39170370 original size:7 final size:8
Alignment explanation
Indices: 39170353--39170377 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
39170343 AAAATATTTT
39170353 AAAAATAA
1 AAAAATAA
39170361 AAAAATAA
1 AAAAATAA
39170369 AAAAATAA
1 AAAAATAA
39170377 A
1 A
39170378 TATTTATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAAATAA
Found at i:39178439 original size:21 final size:21
Alignment explanation
Indices: 39178410--39178459 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
39178400 ACTAGAGTGC
* *
39178410 GTTCTACCGATAGAAGTCTGA
1 GTTCTACCGATAGAACTCTCA
* *
39178431 GTTGTACCGGTAGAACTCTCA
1 GTTCTACCGATAGAACTCTCA
39178452 GTTCTACC
1 GTTCTACC
39178460 AGTAGAATTC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.30
Consensus pattern (21 bp):
GTTCTACCGATAGAACTCTCA
Found at i:39178464 original size:21 final size:20
Alignment explanation
Indices: 39178410--39178466 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 20
39178400 ACTAGAGTGC
* *
39178410 GTTCTACCGATAGAAGTCTGA
1 GTTCTACCG-TAGAACTCTCA
*
39178431 GTTGTACCGGTAGAACTCTCA
1 GTTCTACC-GTAGAACTCTCA
39178452 GTTCTACCAGTAGAA
1 GTTCTACC-GTAGAA
39178467 TTCTGTAGCC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 29 0.97
22 1 0.03
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (20 bp):
GTTCTACCGTAGAACTCTCA
Found at i:39183542 original size:50 final size:50
Alignment explanation
Indices: 39183478--39183670 Score: 230
Period size: 50 Copynumber: 3.9 Consensus size: 50
39183468 ACATTAAGAG
* * *
39183478 GATGAGA--TCCCATGTAAGACCATGTTTGGAACATGGCGTTGACACTGA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACTGA
* *
39183526 GATGAGAGGTCCCATGTAAGACCATGTTTGGGACATGGCGTTGGCACCGA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACTGA
* * * * *
39183576 GATGAGAGGTCCCATGTAAAACCATATCTGGGATATGGCATTGGCAGT-A
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACTGA
* * ** *
39183625 CATGAAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
39183671 TGTTATTATC
Statistics
Matches: 125, Mismatches: 18, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
48 7 0.06
49 39 0.31
50 79 0.63
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (50 bp):
GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACTGA
Found at i:39192109 original size:26 final size:25
Alignment explanation
Indices: 39192052--39192109 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
39192042 AAACCGAAAG
39192052 TAAAAAAAAAATTGATACATATATA
1 TAAAAAAAAAATTGATACATATATA
** * * *
39192077 TCTAAAAACAATTTATAGCATATTTA
1 TAAAAAAAAAATTGATA-CATATATA
39192103 TAAAAAA
1 TAAAAAA
39192110 TTGTACAGTA
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
25 13 0.52
26 12 0.48
ACGTcount: A:0.59, C:0.07, G:0.03, T:0.31
Consensus pattern (25 bp):
TAAAAAAAAAATTGATACATATATA
Found at i:39192338 original size:15 final size:15
Alignment explanation
Indices: 39192318--39192347 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
39192308 CGTGGGAGAC
*
39192318 AAAATTAAGTAAAAA
1 AAAATTAAGGAAAAA
39192333 AAAATTAAGGAAAAA
1 AAAATTAAGGAAAAA
39192348 CAATGGAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.73, C:0.00, G:0.10, T:0.17
Consensus pattern (15 bp):
AAAATTAAGGAAAAA
Found at i:39192723 original size:90 final size:90
Alignment explanation
Indices: 39192622--39192798 Score: 354
Period size: 90 Copynumber: 2.0 Consensus size: 90
39192612 ACCAAATAGA
39192622 TAACATATGTAAAATAATATAATACCATGTTCAAACAAATATCTACAAGAAAATCAAGTAAAAAC
1 TAACATATGTAAAATAATATAATACCATGTTCAAACAAATATCTACAAGAAAATCAAGTAAAAAC
39192687 ATGCTTGAAAGCAATCAAAAGGCGG
66 ATGCTTGAAAGCAATCAAAAGGCGG
39192712 TAACATATGTAAAATAATATAATACCATGTTCAAACAAATATCTACAAGAAAATCAAGTAAAAAC
1 TAACATATGTAAAATAATATAATACCATGTTCAAACAAATATCTACAAGAAAATCAAGTAAAAAC
39192777 ATGCTTGAAAGCAATCAAAAGG
66 ATGCTTGAAAGCAATCAAAAGG
39192799 TGGAAAATAC
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
90 87 1.00
ACGTcount: A:0.52, C:0.14, G:0.11, T:0.23
Consensus pattern (90 bp):
TAACATATGTAAAATAATATAATACCATGTTCAAACAAATATCTACAAGAAAATCAAGTAAAAAC
ATGCTTGAAAGCAATCAAAAGGCGG
Found at i:39196504 original size:28 final size:28
Alignment explanation
Indices: 39196444--39196497 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
39196434 TAGTAACAGT
*
39196444 ACAGTGTGGGCCTTAGCCCAATACATAA
1 ACAGTGTGGGCCTAAGCCCAATACATAA
* *
39196472 ACAGTGTGGGCCTAAGTCCGATACAT
1 ACAGTGTGGGCCTAAGCCCAATACAT
39196498 TATCAGTATG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.30, C:0.24, G:0.24, T:0.22
Consensus pattern (28 bp):
ACAGTGTGGGCCTAAGCCCAATACATAA
Found at i:39196665 original size:26 final size:26
Alignment explanation
Indices: 39196613--39196665 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
39196603 CACCAATATC
* *
39196613 GCAGCATAGCTGCCAGTAGTAATAAT
1 GCAGCAGAGCTGCCAGTAGTAAGAAT
*
39196639 GCAGCAGAGCTGCCAGTAGTCAGAAT
1 GCAGCAGAGCTGCCAGTAGTAAGAAT
39196665 G
1 G
39196666 GCTAAGAGCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.32, C:0.21, G:0.28, T:0.19
Consensus pattern (26 bp):
GCAGCAGAGCTGCCAGTAGTAAGAAT
Found at i:39196713 original size:22 final size:21
Alignment explanation
Indices: 39196659--39196723 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 21
39196649 TGCCAGTAGT
*
39196659 CAGAATGGCTAAGAGCTGTAAA
1 CAGAATGGCTAA-AGCTATAAA
*
39196681 CATG-ATAGCTATAAGCTATAAA
1 CA-GAATGGCTA-AAGCTATAAA
*
39196703 CAGAATGGCTACAAGCCATAA
1 CAGAATGGCTA-AAGCTATAA
39196724 GTACAGTAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
21 1 0.03
22 32 0.91
23 2 0.06
ACGTcount: A:0.43, C:0.17, G:0.20, T:0.20
Consensus pattern (21 bp):
CAGAATGGCTAAAGCTATAAA
Found at i:39196778 original size:32 final size:32
Alignment explanation
Indices: 39196715--39196949 Score: 219
Period size: 32 Copynumber: 7.4 Consensus size: 32
39196705 GAATGGCTAC
* * * *
39196715 AAGCCATAAGT-ACAGTAATGTGATTGGCACA
1 AAGCCATCAGTAACAGTGATATGATCGGCACA
**
39196746 AAGCCATCAGTAGTAGTGATATGATCGGCACA
1 AAGCCATCAGTAACAGTGATATGATCGGCACA
* * * * *
39196778 AAACCATCAGTAACGGTAACATGATCGACACA
1 AAGCCATCAGTAACAGTGATATGATCGGCACA
* *
39196810 AAGCCATCAGTAGCAGTGATATGATTGGCACA
1 AAGCCATCAGTAACAGTGATATGATCGGCACA
*
39196842 CAA-CCATCAGTAACAGTGAAATGATCGGCACA
1 -AAGCCATCAGTAACAGTGATATGATCGGCACA
* * ** *
39196874 CAA-CCATC-GATAACGGTAATATGATTAGTACA
1 -AAGCCATCAG-TAACAGTGATATGATCGGCACA
*
39196906 AAGCCATCAGTAACGGT-ACTATGATCGGCACA
1 AAGCCATCAGTAACAGTGA-TATGATCGGCACA
39196938 AAGCCATCAGTA
1 AAGCCATCAGTA
39196950 GCATCTCAGC
Statistics
Matches: 166, Mismatches: 32, Indels: 11
0.79 0.15 0.05
Matches are distributed among these distances:
31 14 0.08
32 149 0.90
33 3 0.02
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.20
Consensus pattern (32 bp):
AAGCCATCAGTAACAGTGATATGATCGGCACA
Found at i:39196847 original size:64 final size:63
Alignment explanation
Indices: 39196735--39196952 Score: 255
Period size: 64 Copynumber: 3.4 Consensus size: 63
39196725 TACAGTAATG
* * *
39196735 TGATTGGCACAAAGCCATCAGTAGTAGTGATATGATCGGCACAAAACCATCAGTAACGGTAACA
1 TGATCGGCACAAAGCCATCAGTAGCAGTGATATGATTGGCAC-AAACCATCAGTAACGGTAACA
* *
39196799 TGATCGACACAAAGCCATCAGTAGCAGTGATATGATTGGCACACAACCATCAGTAACAGTGAA-A
1 TGATCGGCACAAAGCCATCAGTAGCAGTGATATGATTGGCACA-AACCATCAGTAACGGT-AACA
* * * * *
39196863 TGATCGGCACACAA-CCATC-GATAACGGTAATATGATTAGTACAAAGCCATCAGTAACGGT-AC
1 TGATCGGCACA-AAGCCATCAG-TAGCAGTGATATGATTGGCACAAA-CCATCAGTAACGGTAAC
39196925 TA
63 -A
39196927 TGATCGGCACAAAGCCATCAGTAGCA
1 TGATCGGCACAAAGCCATCAGTAGCA
39196953 TCTCAGCAAA
Statistics
Matches: 131, Mismatches: 14, Indels: 18
0.80 0.09 0.11
Matches are distributed among these distances:
62 1 0.01
63 6 0.05
64 119 0.91
65 5 0.04
ACGTcount: A:0.38, C:0.22, G:0.21, T:0.20
Consensus pattern (63 bp):
TGATCGGCACAAAGCCATCAGTAGCAGTGATATGATTGGCACAAACCATCAGTAACGGTAACA
Found at i:39196851 original size:96 final size:94
Alignment explanation
Indices: 39196715--39196952 Score: 284
Period size: 96 Copynumber: 2.5 Consensus size: 94
39196705 GAATGGCTAC
* * * *
39196715 AAGCCATAAGTACAGTAATGTGATTGGCACAAAGCCATCAGTAGTAGTGATATGATCGGCACAAA
1 AAGCCATCAGTACAGT-ATATGATTGGCACAAAGCCATCAGTAGCAGTGAAATGATCGGCACAAA
39196780 ACCATC-AGTAACGGTAACATGATCGA-CACA
65 ACCATCGA-TAACGGTAACATGAT-GAGCACA
*
39196810 AAGCCATCAGTAGCAGTGATATGATTGGCACACAA-CCATCAGTAACAGTGAAATGATCGGCACA
1 AAGCCATCAGTA-CAGT-ATATGATTGGCACA-AAGCCATCAGTAGCAGTGAAATGATCGGCACA
* * * *
39196874 CAACCATCGATAACGGTAATATGATTAGTACA
63 AAACCATCGATAACGGTAACATGATGAGCACA
* *
39196906 AAGCCATCAGTAACGGTACTATGATCGGCACAAAGCCATCAGTAGCA
1 AAGCCATCAGT-ACAGTA-TATGATTGGCACAAAGCCATCAGTAGCA
39196953 TCTCAGCAAA
Statistics
Matches: 123, Mismatches: 13, Indels: 13
0.83 0.09 0.09
Matches are distributed among these distances:
95 15 0.12
96 104 0.85
97 4 0.03
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (94 bp):
AAGCCATCAGTACAGTATATGATTGGCACAAAGCCATCAGTAGCAGTGAAATGATCGGCACAAAA
CCATCGATAACGGTAACATGATGAGCACA
Found at i:39197167 original size:23 final size:24
Alignment explanation
Indices: 39197121--39197169 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 24
39197111 CCATGCTTAG
*
39197121 AATCAGTTATTCAAATCACAGACA
1 AATCAGTTATTCAAACCACAGACA
*
39197145 AATCAGTTATT-TAACCACAGACA
1 AATCAGTTATTCAAACCACAGACA
39197168 AA
1 AA
39197170 ACAATCATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 12 0.52
24 11 0.48
ACGTcount: A:0.47, C:0.20, G:0.08, T:0.24
Consensus pattern (24 bp):
AATCAGTTATTCAAACCACAGACA
Found at i:39197261 original size:27 final size:27
Alignment explanation
Indices: 39197219--39197493 Score: 325
Period size: 27 Copynumber: 10.2 Consensus size: 27
39197209 CCACCAGGGC
39197219 ATTACGGTCATTTTACCCTACAGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* * * *
39197246 ATTCCGGTTATTTTACCCTATAGGGGC
1 ATTACGGTCATTTTACCCTACAGGGGT
* *
39197273 AGTACGGTCATTTTACCCTACAGGGGC
1 ATTACGGTCATTTTACCCTACAGGGGT
**
39197300 ATTACGACCATTTTACCCTACAGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
** *
39197327 ATTACGACCATTTTACCCTATAGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* * *
39197354 ATTGCGATCATTTTACCCTATAGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
39197381 ATTACGGTCATTTTACCCTACAGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
** * * *
39197408 ATTATAGTTATTTTATCTTACAGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* * *
39197435 ATTAAGGTCTTTTTACCCTACAGGGGC
1 ATTACGGTCATTTTACCCTACAGGGGT
* * *
39197462 AGTACGGTCATTTTATCCTACAGGGGC
1 ATTACGGTCATTTTACCCTACAGGGGT
39197489 ATTAC
1 ATTAC
39197494 AGTCTAGATA
Statistics
Matches: 213, Mismatches: 35, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 213 1.00
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.34
Consensus pattern (27 bp):
ATTACGGTCATTTTACCCTACAGGGGT
Found at i:39197321 original size:81 final size:81
Alignment explanation
Indices: 39197200--39197493 Score: 360
Period size: 81 Copynumber: 3.7 Consensus size: 81
39197190 GGAAAAAATA
*
39197200 GTCA-TTTACCC-ACCA-GGGCATTACGGTCATTTTACCCTACAGGGGTATTCCGGTTATTTTAC
1 GTCATTTTACCCTA-CAGGGGCATTACGGTCATTTTACCCTACAGGGGTATTACGGTTATTTTAC
* *
39197262 CCTATAGGGGCAGTACG
65 CCTATAGGGGTATTACG
** ***
39197279 GTCATTTTACCCTACAGGGGCATTACGACCATTTTACCCTACAGGGGTATTACGACCATTTTACC
1 GTCATTTTACCCTACAGGGGCATTACGGTCATTTTACCCTACAGGGGTATTACGGTTATTTTACC
*
39197344 CTATAGGGGTATTGCG
66 CTATAGGGGTATTACG
* * * ** *
39197360 ATCATTTTACCCTATAGGGGTATTACGGTCATTTTACCCTACAGGGGTATTATAGTTATTTTATC
1 GTCATTTTACCCTACAGGGGCATTACGGTCATTTTACCCTACAGGGGTATTACGGTTATTTTACC
* * *
39197425 TTACAGGGGTATTAAG
66 CTATAGGGGTATTACG
* * * *
39197441 GTCTTTTTACCCTACAGGGGCAGTACGGTCATTTTATCCTACAGGGGCATTAC
1 GTCATTTTACCCTACAGGGGCATTACGGTCATTTTACCCTACAGGGGTATTAC
39197494 AGTCTAGATA
Statistics
Matches: 180, Mismatches: 32, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
79 4 0.02
80 9 0.05
81 167 0.93
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.33
Consensus pattern (81 bp):
GTCATTTTACCCTACAGGGGCATTACGGTCATTTTACCCTACAGGGGTATTACGGTTATTTTACC
CTATAGGGGTATTACG
Found at i:39204456 original size:17 final size:17
Alignment explanation
Indices: 39204423--39204456 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
39204413 CTTAGATTCG
*
39204423 AAAAAAGAAGAGTAAAA
1 AAAAAAGAAGAATAAAA
39204440 AAAAAAGAA-AATAAAA
1 AAAAAAGAAGAATAAAA
39204456 A
1 A
39204457 GTTCGGGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.82, C:0.00, G:0.12, T:0.06
Consensus pattern (17 bp):
AAAAAAGAAGAATAAAA
Found at i:39204901 original size:20 final size:20
Alignment explanation
Indices: 39204876--39204913 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
39204866 GTAATTATAT
39204876 TAATTATATATGTTAAATAA
1 TAATTATATATGTTAAATAA
39204896 TAATTATATATGTTAAAT
1 TAATTATATATGTTAAAT
39204914 CACCAACCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (20 bp):
TAATTATATATGTTAAATAA
Found at i:39207794 original size:28 final size:27
Alignment explanation
Indices: 39207737--39207833 Score: 149
Period size: 27 Copynumber: 3.6 Consensus size: 27
39207727 TAAATTGTGC
* *
39207737 AGCACTAAGTGTGCGAATTGAATATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
39207764 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
*
39207792 AGCACTAAGTGTGCGAGTTGACTATAT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
39207819 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
39207834 GACTTAATAA
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
27 39 0.60
28 26 0.40
ACGTcount: A:0.28, C:0.14, G:0.29, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGACTATGT
Found at i:39224964 original size:25 final size:25
Alignment explanation
Indices: 39224922--39224996 Score: 87
Period size: 26 Copynumber: 2.9 Consensus size: 25
39224912 TTTCTCACCC
*
39224922 AATTTGAACCTGGTAAAATTTTGACG
1 AATTT-AACCCGGTAAAATTTTGACG
*
39224948 AATTTAACCCGGAAAAAATTTTGACG
1 AATTTAACCCGG-TAAAATTTTGACG
* * *
39224974 ATTTTACCCCAGTAAAATTTTGA
1 AATTTAACCCGGTAAAATTTTGA
39224997 GAAAATTTGT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
25 16 0.38
26 26 0.62
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (25 bp):
AATTTAACCCGGTAAAATTTTGACG
Found at i:39227538 original size:28 final size:27
Alignment explanation
Indices: 39227460--39227539 Score: 106
Period size: 27 Copynumber: 2.9 Consensus size: 27
39227450 TGGGGTGAAC
* *
39227460 AATAAAAAGAAAGCCTTGGTGGCAAAC
1 AATAAAAAGAAAGCCTTTGTGGCAAAA
* *
39227487 CATGAAAAGAAAGCCTTTGTGGCAAAA
1 AATAAAAAGAAAGCCTTTGTGGCAAAA
*
39227514 AATAAAAAGATTAGCCTTTGTGGCAA
1 AATAAAAAGA-AAGCCTTTGTGGCAA
39227540 TCATCTGAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
27 31 0.69
28 14 0.31
ACGTcount: A:0.45, C:0.14, G:0.21, T:0.20
Consensus pattern (27 bp):
AATAAAAAGAAAGCCTTTGTGGCAAAA
Found at i:39231216 original size:16 final size:16
Alignment explanation
Indices: 39231186--39231218 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
39231176 AGAGACCGAT
39231186 TGGACATATGTAATTA
1 TGGACATATGTAATTA
39231202 TGGATCATATG-AATTA
1 TGGA-CATATGTAATTA
39231218 T
1 T
39231219 AATTAAGTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.36, C:0.06, G:0.18, T:0.39
Consensus pattern (16 bp):
TGGACATATGTAATTA
Found at i:39238105 original size:27 final size:26
Alignment explanation
Indices: 39238058--39238111 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 26
39238048 TGTCTTATTA
*
39238058 ATTAATTATACTTAAACTAATTAAACT
1 ATTAATCATACTTAAACTAA-TAAACT
*
39238085 ATTAATCATACTATATA-TAATAAACT
1 ATTAATCATACT-TAAACTAATAAACT
39238111 A
1 A
39238112 GTGGAAGGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 7 0.29
27 14 0.58
28 3 0.12
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (26 bp):
ATTAATCATACTTAAACTAATAAACT
Found at i:39238778 original size:4 final size:4
Alignment explanation
Indices: 39238769--39239890 Score: 1954
Period size: 4 Copynumber: 281.0 Consensus size: 4
39238759 TTCGAGTTCA
* *
39238769 ATGT ATGT ATGT ATGT ATGT ATGT ATG- -TGT GTGT GTGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* *
39238815 GTGT ATG- -TGT GTGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
*
39238861 ATGT ATGT ATGT ATGTT AATGT ATGT ATGT ATGT ATGT TTGT ATGT ATGAT
1 ATGT ATGT ATGT ATG-T -ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATG-T
39238912 AATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 -ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
39238961 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
*
39239009 ATGT ATGT ATGT ATGT ATGT ATGT ATAT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * * * *
39239057 ATG- -TGT GTGT ATGT GTGT GTGT ATGT GTGT GTGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
39239103 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * *
39239151 ATGT ATGT ATGT ATG- -TGT GTGT ATGT ATGT ATGT GTGT GTGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * *
39239197 GTGT GTGT GTGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
39239245 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
39239293 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
39239341 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
39239389 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
39239437 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
39239485 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
39239533 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
39239581 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
39239629 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
39239677 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
39239725 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
39239773 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * *
39239821 ATGT ATGT ATGT ATGT ATGT TTGT ATGTT AATGT TTTT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATG-T -ATGT ATGT ATGT ATGT ATGT
39239871 ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT
39239891 TAATGTTTTT
Statistics
Matches: 1080, Mismatches: 24, Indels: 28
0.95 0.02 0.02
Matches are distributed among these distances:
2 8 0.01
4 1057 0.98
5 6 0.01
6 9 0.01
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:39239935 original size:22 final size:20
Alignment explanation
Indices: 39239886--39239929 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
39239876 TGTATGTATG
39239886 TATGTTAATGTTTTTTCTTA
1 TATGTTAATGTTTTTTCTTA
39239906 TATGTTAATGTTTTTTCTTA
1 TATGTTAATGTTTTTTCTTA
39239926 TATG
1 TATG
39239930 ACTTAAATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.20, C:0.05, G:0.11, T:0.64
Consensus pattern (20 bp):
TATGTTAATGTTTTTTCTTA
Found at i:39243768 original size:73 final size:73
Alignment explanation
Indices: 39243686--39243831 Score: 265
Period size: 73 Copynumber: 2.0 Consensus size: 73
39243676 CTTCTAATTT
* *
39243686 TCAACTCTAACAAGCAATGCATGGAAAGAAAAAGTTATTTTCTTACCAATTTTCTGTCTCTCCTA
1 TCAACTCTAACAAGCAATGCATGGAAAGAAAAAGTGATTTTCTTACCAATTTTCCGTCTCTCCTA
39243751 CCAAGCAC
66 CCAAGCAC
*
39243759 TCAACTCTAACAAGCAATGCATGGAAAGAAAAAGTGATTTTCTTACCATTTTTCCGTCTCTCCTA
1 TCAACTCTAACAAGCAATGCATGGAAAGAAAAAGTGATTTTCTTACCAATTTTCCGTCTCTCCTA
39243824 CCAAGCAC
66 CCAAGCAC
39243832 ACATATCGTC
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
73 70 1.00
ACGTcount: A:0.34, C:0.25, G:0.12, T:0.29
Consensus pattern (73 bp):
TCAACTCTAACAAGCAATGCATGGAAAGAAAAAGTGATTTTCTTACCAATTTTCCGTCTCTCCTA
CCAAGCAC
Found at i:39244200 original size:18 final size:20
Alignment explanation
Indices: 39244159--39244200 Score: 52
Period size: 18 Copynumber: 2.2 Consensus size: 20
39244149 ACAAACTGTG
*
39244159 AAAACACAAGCAAATAAAAG
1 AAAACACAAGCAAATAAAAC
*
39244179 AAAACA-AAGCTAA-AAAAC
1 AAAACACAAGCAAATAAAAC
39244197 AAAA
1 AAAA
39244201 TAGAATATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 8 0.40
19 6 0.30
20 6 0.30
ACGTcount: A:0.74, C:0.14, G:0.07, T:0.05
Consensus pattern (20 bp):
AAAACACAAGCAAATAAAAC
Found at i:39244501 original size:15 final size:15
Alignment explanation
Indices: 39244481--39244510 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
39244471 GAGAGAAAAC
*
39244481 TGAGAGAAAACAGAA
1 TGAGAGAAAAAAGAA
39244496 TGAGAGAAAAAAGAA
1 TGAGAGAAAAAAGAA
39244511 GCTGAAAACA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.03, G:0.27, T:0.07
Consensus pattern (15 bp):
TGAGAGAAAAAAGAA
Found at i:39249454 original size:15 final size:15
Alignment explanation
Indices: 39249434--39249463 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
39249424 GAGAGAAAAC
*
39249434 TGAGAGAAAATAGAA
1 TGAGAGAAAAAAGAA
39249449 TGAGAGAAAAAAGAA
1 TGAGAGAAAAAAGAA
39249464 GCTGAAAACA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.27, T:0.10
Consensus pattern (15 bp):
TGAGAGAAAAAAGAA
Found at i:39251027 original size:21 final size:22
Alignment explanation
Indices: 39250998--39251038 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
39250988 TGGTTGAACT
*
39250998 AATTTTTTAATATTT-TTTATA
1 AATTATTTAATATTTATTTATA
39251019 AATTATTTAATATTTATTTA
1 AATTATTTAATATTTATTTA
39251039 ATCAAACCGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
AATTATTTAATATTTATTTATA
Found at i:39251928 original size:9 final size:9
Alignment explanation
Indices: 39251914--39251939 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
39251904 GCTGGACTAA
39251914 CTTTCTTCC
1 CTTTCTTCC
39251923 CTTTCTTCC
1 CTTTCTTCC
39251932 CTTTCTTC
1 CTTTCTTC
39251940 TTGCCTCCCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (9 bp):
CTTTCTTCC
Found at i:39261301 original size:18 final size:18
Alignment explanation
Indices: 39261262--39261304 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
39261252 CATTTAATTT
*
39261262 CATTTC-ATAACATTTGT
1 CATTTCAATAACATTTGC
* *
39261279 TATTTCAATATCATTTGC
1 CATTTCAATAACATTTGC
39261297 CATTTCAA
1 CATTTCAA
39261305 GTCATTAACT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.30, C:0.19, G:0.05, T:0.47
Consensus pattern (18 bp):
CATTTCAATAACATTTGC
Found at i:39264645 original size:38 final size:36
Alignment explanation
Indices: 39264561--39264657 Score: 115
Period size: 38 Copynumber: 2.6 Consensus size: 36
39264551 CAAATATAAT
* * *
39264561 AATTATAATTACCATAATTAGAATGTTTGATCGAAA
1 AATTATAATTACAATAATTATAATATTTGATCGAAA
* *
39264597 AATTACAATTACAATAATTATAATAATATTCGATC-ATA
1 AATTATAATTACAATAATTATAAT-AT-TT-GATCGAAA
39264635 AATTATAATTACAATAATTATAA
1 AATTATAATTACAATAATTATAA
39264658 CAAGGATTTC
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
36 21 0.40
37 1 0.02
38 26 0.50
39 4 0.08
ACGTcount: A:0.49, C:0.08, G:0.05, T:0.37
Consensus pattern (36 bp):
AATTATAATTACAATAATTATAATATTTGATCGAAA
Found at i:39267418 original size:22 final size:22
Alignment explanation
Indices: 39267376--39267442 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 22
39267366 AATCGAAATG
39267376 AATA-AAAATTTTA-AAACATA
1 AATATAAAATTTTATAAACATA
*
39267396 AA-ATAAAATTTTATAAATTATA
1 AATATAAAATTTTATAAA-CATA
39267418 AATTATAATACATTTTATAAACATA
1 AA-TATAA-A-ATTTTATAAACATA
39267443 TACATATATT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
19 1 0.03
20 11 0.29
21 3 0.08
22 5 0.13
24 4 0.11
25 4 0.11
26 10 0.26
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.37
Consensus pattern (22 bp):
AATATAAAATTTTATAAACATA
Found at i:39267680 original size:104 final size:104
Alignment explanation
Indices: 39267560--39267771 Score: 415
Period size: 104 Copynumber: 2.0 Consensus size: 104
39267550 TGATTTATTA
39267560 AAAAAAACTTTCGAAATCAAAATTAAATATGAAAAGTATTTTGAAGTTGAAAATAATAATCAACA
1 AAAAAAACTTTCGAAATCAAAATTAAATATGAAAAGTATTTTGAAGTTGAAAATAATAATCAACA
39267625 AATTTTAAATCGAGGTTTAAATAAAATTAAATTAATAAT
66 AATTTTAAATCGAGGTTTAAATAAAATTAAATTAATAAT
*
39267664 AAAAAAACTTTTGAAATCAAAATTAAATATGAAAAGTATTTTGAAGTTGAAAATAATAATCAACA
1 AAAAAAACTTTCGAAATCAAAATTAAATATGAAAAGTATTTTGAAGTTGAAAATAATAATCAACA
39267729 AATTTTAAATCGAGGTTTAAATAAAATTAAATTAATAAT
66 AATTTTAAATCGAGGTTTAAATAAAATTAAATTAATAAT
39267768 AAAA
1 AAAA
39267772 GAAGACAAAA
Statistics
Matches: 107, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
104 107 1.00
ACGTcount: A:0.55, C:0.05, G:0.08, T:0.32
Consensus pattern (104 bp):
AAAAAAACTTTCGAAATCAAAATTAAATATGAAAAGTATTTTGAAGTTGAAAATAATAATCAACA
AATTTTAAATCGAGGTTTAAATAAAATTAAATTAATAAT
Found at i:39274274 original size:20 final size:20
Alignment explanation
Indices: 39274249--39274294 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
39274239 TCTCTCAACA
39274249 AAAATTACAAAATAATTTTC
1 AAAATTACAAAATAATTTTC
** *
39274269 AAAATTTTAAAATAATTTTT
1 AAAATTACAAAATAATTTTC
39274289 AAAATT
1 AAAATT
39274295 TAAAATATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.41
Consensus pattern (20 bp):
AAAATTACAAAATAATTTTC
Found at i:39274298 original size:19 final size:20
Alignment explanation
Indices: 39274257--39274310 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
39274247 CAAAAATTAC
*
39274257 AAAATAATTTTCAAAATTTT
1 AAAATAATTTTTAAAATTTT
39274277 AAAATAATTTTTAAAA-TTT
1 AAAATAATTTTTAAAATTTT
*
39274296 AAAAT-ATTTATAAAA
1 AAAATAATTTTTAAAA
39274311 AATTCCAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.28
19 8 0.25
20 15 0.47
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (20 bp):
AAAATAATTTTTAAAATTTT
Found at i:39274311 original size:19 final size:19
Alignment explanation
Indices: 39274257--39274311 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 19
39274247 CAAAAATTAC
*
39274257 AAAATAATTTTCAAAATTTT
1 AAAATAATTTT-AAAAATTT
*
39274277 AAAATAATTTTTAAAATTT
1 AAAATAATTTTAAAAATTT
39274296 AAAAT-ATTTATAAAAA
1 AAAATAATTT-TAAAAA
39274312 ATTCCAAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
18 4 0.13
19 16 0.52
20 11 0.35
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (19 bp):
AAAATAATTTTAAAAATTT
Found at i:39274312 original size:20 final size:19
Alignment explanation
Indices: 39274289--39274327 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
39274279 AATAATTTTT
*
39274289 AAAATTTAAAATATTTATAA
1 AAAATTCAAAAT-TTTATAA
*
39274309 AAAATTCCAAATTTTATAA
1 AAAATTCAAAATTTTATAA
39274328 TTTTGAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAATTCAAAATTTTATAA
Found at i:39278472 original size:24 final size:24
Alignment explanation
Indices: 39278445--39278490 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
39278435 TGGTATGGAA
39278445 GATAAAGTTTGTAACCTTCAGGTT
1 GATAAAGTTTGTAACCTTCAGGTT
39278469 GATAAAGTTTGTAACCTTCAGG
1 GATAAAGTTTGTAACCTTCAGG
39278491 ATTTGTGGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.35
Consensus pattern (24 bp):
GATAAAGTTTGTAACCTTCAGGTT
Found at i:39291661 original size:52 final size:52
Alignment explanation
Indices: 39291583--39291688 Score: 212
Period size: 52 Copynumber: 2.0 Consensus size: 52
39291573 CATCACCAAT
39291583 CTTTACATCAAACCCAAAACTAGTTTTATCTTTCTCCAAGGAGAGAGTTCAA
1 CTTTACATCAAACCCAAAACTAGTTTTATCTTTCTCCAAGGAGAGAGTTCAA
39291635 CTTTACATCAAACCCAAAACTAGTTTTATCTTTCTCCAAGGAGAGAGTTCAA
1 CTTTACATCAAACCCAAAACTAGTTTTATCTTTCTCCAAGGAGAGAGTTCAA
39291687 CT
1 CT
39291689 CACATGCTCG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 54 1.00
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.31
Consensus pattern (52 bp):
CTTTACATCAAACCCAAAACTAGTTTTATCTTTCTCCAAGGAGAGAGTTCAA
Found at i:39293098 original size:11 final size:10
Alignment explanation
Indices: 39293056--39293109 Score: 63
Period size: 11 Copynumber: 5.0 Consensus size: 10
39293046 AACTTAATAC
39293056 TTTCTCTCAA
1 TTTCTCTCAA
39293066 TTTCTCTCTAA
1 TTTCTCTC-AA
39293077 TATTCTCTCAAA
1 T-TTCTCTC-AA
*
39293089 TTTGTCTCAA
1 TTTCTCTCAA
39293099 TTTCCTCTCAA
1 TTT-CTCTCAA
39293110 ATTCCTATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
10 13 0.34
11 15 0.39
12 10 0.26
ACGTcount: A:0.22, C:0.28, G:0.02, T:0.48
Consensus pattern (10 bp):
TTTCTCTCAA
Found at i:39293110 original size:22 final size:23
Alignment explanation
Indices: 39293057--39293112 Score: 73
Period size: 22 Copynumber: 2.5 Consensus size: 23
39293047 ACTTAATACT
39293057 TTCTCTC-AATTTCTCTCTAATA
1 TTCTCTCAAATTTCTCTCTAATA
*
39293079 TTCTCTCAAATTTGTCTC-AAT-
1 TTCTCTCAAATTTCTCTCTAATA
39293100 TTCCTCTCAAATT
1 TT-CTCTCAAATT
39293113 CCTATTTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 2 0.06
22 20 0.65
23 9 0.29
ACGTcount: A:0.23, C:0.27, G:0.02, T:0.48
Consensus pattern (23 bp):
TTCTCTCAAATTTCTCTCTAATA
Found at i:39293166 original size:28 final size:26
Alignment explanation
Indices: 39293117--39293174 Score: 64
Period size: 29 Copynumber: 2.2 Consensus size: 26
39293107 CAAATTCCTA
*
39293117 TTTTAAAAAGCTTTAATTTTTTAATTAT
1 TTTTAAAAAGCTTTAATATTTT-ATT-T
*
39293145 TTTTAAAAAAGTTTTAA-ATTTTATTT
1 TTTT-AAAAAGCTTTAATATTTTATTT
39293171 TTTT
1 TTTT
39293175 GAATCTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 5 0.19
27 3 0.11
28 8 0.30
29 11 0.41
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.60
Consensus pattern (26 bp):
TTTTAAAAAGCTTTAATATTTTATTT
Found at i:39294282 original size:7 final size:7
Alignment explanation
Indices: 39294270--39294302 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
39294260 TAGTCAATTG
39294270 GTATTTA
1 GTATTTA
39294277 GTATTTA
1 GTATTTA
39294284 GTATTTA
1 GTATTTA
*
39294291 GTATTCA
1 GTATTTA
39294298 GTATT
1 GTATT
39294303 ATGCATTATG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.27, C:0.03, G:0.15, T:0.55
Consensus pattern (7 bp):
GTATTTA
Found at i:39294978 original size:18 final size:18
Alignment explanation
Indices: 39294955--39294992 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
39294945 TGCCAAGTGC
* *
39294955 GTATCCTAGCCCTTTTAT
1 GTATCCTAACCCTTATAT
39294973 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
39294991 GT
1 GT
39294993 TTCTTTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:39295255 original size:21 final size:21
Alignment explanation
Indices: 39295204--39295267 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
39295194 CCCAACACCG
* *
39295204 ACAACCAGATTCCCTACCGGA
1 ACAACCAGAATCCCCACCGGA
**
39295225 GGAACCAGAATCCCCACCGGA
1 ACAACCAGAATCCCCACCGGA
* * *
39295246 ACAACTAGAACCCCCGCCGGA
1 ACAACCAGAATCCCCACCGGA
39295267 A
1 A
39295268 GTTGGACAAA
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.34, C:0.39, G:0.19, T:0.08
Consensus pattern (21 bp):
ACAACCAGAATCCCCACCGGA
Done.